Yellowfin tuna (Thunnus albacares) is a highly migratory species that distribute from tropical to subtropical waters. This species can be found in the Atlantic, Indian and Pacific Oceans. Genetic information in fish with long distance migration such as tuna is very important for sustainable use. This study aims to obtain information on genetic diversity and population structure exploited and kinship of yellowfin tuna populations in Indonesian waters. Genetic sampling of yellowfin tuna was conducted in three locations in Indonesian waters in western Sumatra, southern Bali and North Sulawesi waters. The methods used was microsatellite analysis which consist of extraction, purification, polymerase chain reaction (PCR) amplification and electrophoresis. The result of 3 microsatellite DNA locus analysis showed that the level of kinship between the three sample groups in Indonesian waters was relatively close, ranging from 0.132 to 0.206. This shows that yellowfin tuna population in Indonesian waters is a single stock and random copulation. However, as a highly migratory species that migrate across the nations, yellowfin tuna management also requires good cooperation among countries incorporated in regional tuna fisheries management organizations.